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CRAPome specifications


Unique identifier OMICS_16242
Name CRAPome
Alternative name Contaminant Repository for Affinity Purification
Restrictions to use None
Database management system MySQL, SQLite
Community driven No
Data access Browse
User data submission Allowed
Version 1.1
Maintained Yes


  • person_outline Alexey Nesvizhskii

Publication for Contaminant Repository for Affinity Purification

CRAPome citations


PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia

PMCID: 5955148
PMID: 29774127
DOI: 10.18632/oncotarget.25204

[…] DC73 or FLAG-CDC73_3YF. Co-IPs from M1 cells were analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS). Using the Contaminant Repository for Affinity Purification online resource (CRAPome), protein-protein interactions were scored using Significance Analysis of Interactome (SAINT) probabilistic scoring (Figure , ). Interestingly, there was a distinct subset of 87 potential CDC7 […]


An AP MS and BioID compatible MAC tag enables comprehensive mapping of protein interactions and subcellular localizations

Nat Commun
PMCID: 5864832
PMID: 29568061
DOI: 10.1038/s41467-018-03523-2

[…] Significance Analysis of INTeractome (SAINT)-express version 3.6.0, and Contaminant Repository for Affinity Purification (CRAPome, were used as statistical tools for identification of specific high-confidence interactions from our AP-MS data. 16 G […]


The interferon stimulated gene product oligoadenylate synthetase like protein enhances replication of Kaposi’s sarcoma associated herpesvirus (KSHV) and interacts with the KSHV ORF20 protein

PLoS Pathog
PMCID: 5851652
PMID: 29499066
DOI: 10.1371/journal.ppat.1006937

[…] ction partners of both ORF20 and OASL. Ribosomal proteins are often considered contaminants in standard affinity purification mass spectrometry analysis and many ribosomal proteins are listed in the “contaminant repository for affinity purification”, or CRAPome []. However, q-AP-MS allows identification of ribosomal proteins as specific interaction partners. True interaction partners are identifie […]


The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics

PMCID: 5891429
PMID: 29467281
DOI: 10.15252/embr.201744884
call_split See protocol

[…] contaminants and intensity values were log10 transformed. For label‐free experiments, data were uploaded to the online analysis tool , . The default settings were used for all analysis in CRAPome (FC‐A, user, default, average; FC‐B, all, stringent, geometric; SAINT‐express, user, average, virtual controls 10, all replicates). Scores were downloaded and exported to ProHits‐Viz to make d […]


2‐anilino‐4‐amino‐5‐aroylthiazole‐type compound AS7128 inhibits lung cancer growth through decreased iASPP and p53 interaction

Cancer Sci
PMCID: 5834782
PMID: 29285847
DOI: 10.1111/cas.13489
call_split See protocol

[…] g the Mascot search engine against the Swiss‐Prot Homo sapiens protein database. Non‐specific binding protein were eliminated from control group first. The remaining interactors were mapped using the CRAPome database and a recent study to determine the contaminant frequency of observations across AP‐MS; and those frequency more than 15% were also be eliminated as the non‐specific binders in this f […]


ER associated degradation regulates Alzheimer’s amyloid pathology and memory function by modulating γ secretase activity

Nat Commun
PMCID: 5684335
PMID: 29133892
DOI: 10.1038/s41467-017-01799-4
call_split See protocol

[…] -based false discovery rate (FDR) filter for spectrum and protein identification was set to 1%. Second peptide mode of MaxQuant software was also enabled. Identified proteins were queried against the Crapome database comprised of 411 experiments. A heatmap was generated using the R Bioconductor gplots package. […]


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CRAPome funding source(s)
This work was supported by the National Institutes of Health (grants n°5R01GM94231, DP1DA026192 and HL112618-01), the Canadian Institutes of Health Research (grants n°MOP84314, MOP82851), the government of Ontario via a Global Leadership Round in Genomics and Life Sciences, the Austrian Academy of Sciences, the Austrian Federal Ministry for Science and Research (grants n°820965 and 820962), the European Research Council (grant n°ERC-2009-AdG-250179-i-FIVE), the Austrian Science Fund FWF (grants n°P24321B21 and P22282B11), the European Molecular Biology Organisation long-term fellowship (grant n°ATLF4632008), The Netherlands Proteomics Center, the European Union 7th Framework Program (grant n°262067), the Stowers Institute for Medical Research, the Human Frontier Science Program (RGY0079/2009-C to IMC), the Cleveland Foundation, NIH (grant n°1R21CA16006001A1), the Canadian Institute for Health Research and TD Bank.

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